6GEH

Structure and reactivity of a siderophore-interacting protein from the marine bacterium Shewanella reveals unanticipated functional versatility.

• PDB DOI:  https://doi.org/10.2210/pdb6GEH/pdb

• Classification: METAL TRANSPORT
• Organism(s): Shewanella frigidimarina NCIMB 400
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-04-26 Released: 2018-11-21 
• Deposition Author(s): Trindade, I.B., Silva, J.P.M., Matias, P., Moe, E.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 0.173 
• R-Value Work: 0.145 
• R-Value Observed: 0.146 

Literature

Structure and reactivity of a siderophore-interacting protein from the marine bacteriumShewanellareveals unanticipated functional versatility.

Trindade, I.B., Silva, J.M., Fonseca, B.M., Catarino, T., Fujita, M., Matias, P.M., Moe, E., Louro, R.O.

(2019) J Biol Chem 294: 157-167

• PubMed: 30420426 
• DOI: https://doi.org/10.1074/jbc.RA118.005041
• Primary Citation of Related Structures:  
  6GEH


• PubMed Abstract: 
  

Siderophores make iron accessible under iron-limited conditions and play a crucial role in the survival of microorganisms. Because of their remarkable metal-scavenging properties and ease in crossing cellular envelopes, siderophores hold great potential in biotechnological applications, raising the need for a deeper knowledge of the molecular mechanisms underpinning the siderophore pathway. Here, we report the structural and functional characterization of a siderophore-interacting protein from the marine bacterium Shewanella frigidimarina NCIBM400 (SfSIP). SfSIP is a flavin-containing ferric-siderophore reductase with FAD- and NAD(P)H-binding domains that have high homology with other characterized SIPs. However, we found here that it mechanistically departs from what has been described for this family of proteins. Unlike other FAD-containing SIPs, SfSIP did not discriminate between NADH and NADPH. Furthermore, SfSIP required the presence of the Fe ²⁺ -scavenger, ferrozine, to use NAD(P)H to drive the reduction of Shewanella -produced hydroxamate ferric-siderophores. Additionally, this is the first SIP reported that also uses a ferredoxin as electron donor, and in contrast to NAD(P)H, its utilization did not require the mediation of ferrozine, and electron transfer occurred at fast rates. Finally, FAD oxidation was thermodynamically coupled to deprotonation at physiological pH values, enhancing the solubility of ferrous iron. On the basis of these results and the location of the SfSIP gene downstream of a sequence for putative binding of aerobic respiration control protein A (ArcA), we propose that SfSIP contributes an additional layer of regulation that maintains cellular iron homeostasis according to environmental cues of oxygen availability and cellular iron demand.

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Related Citations: 

• A putative siderophore-interacting protein from the marine bacterium Shewanella frigidimarina NCIMB 400: cloning, expression, purification, crystallization and X-ray diffraction analysis.
  Trindade, I.B., Fonseca, B.M., Matias, P.M., Louro, R.O., Moe, E.
  (2016) Acta Crystallogr F Struct Biol Commun 72: 667

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Organizational Affiliation: 

Instituto de Tecnologia Química e Biológica António Xavier (ITQB-NOVA), Universidade Nova de Lisboa, Av. da República (EAN), 2780-157 Oeiras, Portugal. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 30.36 kDa 
• Atom Count: 2,865 
• Modelled Residue Count: 256 
• Deposited Residue Count: 256 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FAD-binding 9, siderophore-interacting domain protein	A	256	Shewanella frigidimarina NCIMB 400	Mutation(s): 0  Gene Names: Sfri_2392
UniProt
Find proteins for Q080S8 (Shewanella frigidimarina (strain NCIMB 400)) Explore Q080S8  Go to UniProtKB:  Q080S8

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	JA [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
GOL	IA [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS	F [auth A], G [auth A], H [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
FMT	I [auth A], J [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
MG	B [auth A], C [auth A], D [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	AA [auth A], BA [auth A], CA [auth A], DA [auth A], EA [auth A], FA [auth A], GA [auth A], HA [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 0.173 
• R-Value Work: 0.145 
• R-Value Observed: 0.146 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.098	α = 90
b = 77.753	β = 109.64
c = 44.917	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-11-21 
Deposition Author(s): Trindade, I.B., Silva, J.P.M., Matias, P., Moe, E.

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Funding Organization	Location	Grant Number
Other government	Portugal	xx

Revision History  

• Version 1.0: 2018-11-21
  Type: Initial release
  
• Version 1.1: 2019-01-16
  Changes: Data collection, Database references